It took me a while to find out that with Ubuntu One I can sync only folders in my home folder. On all other folders the Ubuntu One option is available in preferences, but the actual actions are greyed out.

The Ubuntu One FAQ is quite clear on that:

No, currently you can only select to synchronize folders inside your home directory.

But I actually wonder why and if this is going to change and if there is a trick around it (an other one than setting my home to /) ?

I personally don't have any important data in my home folder other than the program configs. All documents, pictures, music are on a folder called /data that is actually on a different partition. That makes it much easier when one wants to reinstall Ubuntu.